spcal.datafile

File import and data access.

class spcal.datafile.SPCalDataFile(format: str, path: Path, times: ndarray)

A base class for data files.

exclusion_regions

array of start, end times to exclude from processing. These regions are set to NaN, shape (…, 2)

dataForExpression(expr: SPCalIsotopeExpression) → ndarray

Calculate the result for expr.

dataForIsotope(isotope: SPCalIsotope) → ndarray

Access signals for isotope.

property event_time: float

The time of a single acuqisition. Sometimes called the ‘dwell time’.

isTOF() → bool

Returns True is file is ‘suspected’ of being from a ToF.

property isotopes: list[SPCalIsotope]

The number of isotopes. This may be differetn from the number of masses due to isobars.

property masses: ndarray

Masses (m/z) in the data file.

property num_events: int

The number of events (e.g. acquisitions).

property preferred_isotopes: list[SPCalIsotope]

Returns the default isotope for each element.

property selected_isotopes: list[SPCalIsotope]

Currently selected isotopes.

property signals: ndarray

Signal intensities in the data file. Has the shape (num_events, masses).

spectra(regions: ndarray) → ndarray

Access the entire mass spectra between regions.

Parameters:

regions – array start, end points of shape (N, 2)

Returns:

array of spectra shape (N, masses)

property total_time: float

The total time in seconds, excluding NaN regions.

class spcal.datafile.SPCalNuDataFile(path: Path, signals: ndarray, times: ndarray, masses: ndarray, info: dict, cycle_number: int | None, segment_number: int | None, integ_files: tuple[int, int | None], autoblanking: str = 'regions', max_mass_diff: float = 0.05)

Data file for data from a Nu Instruments Vitesse.

Create using the SPCalNuDataFile.load function.

isotope_table

dict of isotopes to their index in signals

dataForIsotope(isotope: SPCalIsotope) → ndarray

Access signals for isotope.

property event_time: float

The time of a single acuqisition. Sometimes called the ‘dwell time’.

generateIsotopeTable()

Populates isotope_table with all available isotopes.

Multiple isotopes may map to the same index in signals if they are isobars.

property isotopes: list[SPCalIsotope]

The number of isotopes. This may be differetn from the number of masses due to isobars.

classmethod load(path: Path | str, max_mass_diff: float = 0.05, cycle_number: int | None = None, segment_number: int | None = None, first_integ_file: int = 0, last_integ_file: int | None = None, autoblank: str = 'regions') → SPCalNuDataFile

Import Nu Instruments Vitesse data.

Parameters:

  • path – Path to the ‘run.info’ file or the containing directory.

  • max_mass_diff – maximum difference (in Da) used for match m/z value to isotopes

  • cycle_number – limit import to a cycle, default to all

  • segment_number – limit import to a segment, default to all

  • first_integ_file – import .integ files starting from this number

  • last_integ_file – import .integ files ending at this number, None for all

  • autoblank – apply autoblanking to overrange regions or to all masses, one of ‘off’, ‘regions’, ‘all’

property masses: ndarray

Masses (m/z) in the data file.

property num_events: int

The number of events (e.g. acquisitions).

property signals: ndarray

Signal intensities in the data file. Has the shape (num_events, masses).

class spcal.datafile.SPCalTOFWERKDataFile(path: Path, signals: ndarray, times: ndarray, peak_table: ndarray, attrs: dict[str, str] | None = None)

Data file for TOFWERK style data.

Create using the SPCalTOFWERKDataFile.load function.

isotope_table

dict of isotopes to signal indicies

dataForIsotope(isotope: SPCalIsotope) → ndarray

Access signals for isotope.

property event_time: float

The time of a single acuqisition. Sometimes called the ‘dwell time’.

property isotopes: list[SPCalIsotope]

The number of isotopes. This may be differetn from the number of masses due to isobars.

classmethod load(path: Path | str, max_size: int | None = None) → SPCalTOFWERKDataFile

Import a TOFWERK .h5 file.

Parameters:

  • path – Path to the .h5

  • max_size – maximum number of events to read

Returns:

data file

property masses: ndarray

Masses (m/z) in the data file.

property num_events: int

The number of events (e.g. acquisitions).

property signals: ndarray

Signal intensities in the data file. Has the shape (num_events, masses).

class spcal.datafile.SPCalTextDataFile(path: Path, signals: ndarray, times: ndarray, isotope_table: dict[SPCalIsotope, str], delimiter: str = ',', skip_rows: int = 1, cps: bool = False, drop_fields: list[str] | None = None, override_event_time: float | None = None)

Import and access to data stored as a text file, such as a CSV.

Create using the SPCalTextDataFile.load function.

dataForIsotope(isotope: SPCalIsotope) → ndarray

Access signals for isotope.

isTOF() → bool

Returns True is file is ‘suspected’ of being from a ToF.

property isotopes: list[SPCalIsotope]

The number of isotopes. This may be differetn from the number of masses due to isobars.

classmethod load(path: Path | str, isotope_table: dict[SPCalIsotope, str] | None = None, delimiter: str = ',', skip_rows: int = 1, cps: bool = False, drop_fields: list[str] | None = None, override_event_time: float | None = None) → SPCalTextDataFile

Imports single particle data stored in a text file.

If a column with ‘time’ in the header is present then the ‘event_time’ can be automatically determined, otherwise override_event_time is required. If more than one isotopes are imported, the file is assumed to be from a ToF.

Parameters:

  • path – path to the file

  • isotope_table – dictionary mmaping an SPCalIsotope to a column name. Note that this uses the name post import via np.genfromtxt.

  • delimiter – the text / column delimiter

  • skip_rows – number of rows to skip, including the header

  • cps – convert counts-per-second into counts, required if file is CPS

  • drop_fields – names in the file to skip. By default names containing ‘index’ or ‘time’ are skipped.

  • override_event_time – override any automatically determined event-time

Returns:

data file

Raises:

ValueError is event time cannot be read and is not provided –

property masses: ndarray

Masses (m/z) in the data file.

property num_events: int

The number of events (e.g. acquisitions).

property signals: ndarray

Signal intensities in the data file. Has the shape (num_events, masses).